Sunday, December 19, 2010

Protein Folding and Evolution

Proteins consist of hundreds of amino acids attached to each other like train cars, and when they fold up they consistently find the same three dimensional shape. Like a necklace that magically falls into the same shape every time it is dropped onto a table, the consistency of protein folding once seemed like a paradox. For there is an astronomical number of shapes the protein could possibly take on. How does it find the same one so consistently, and so quickly? The answer has interesting implications for evolution.

When a protein folds to a given shape, it is fighting nature’s tendency toward disorder. The protein faces a universe of possible shapes, how does it always fold up to the same one? The answer is that this entropy barrier is overcome by the many chemical interactions tugging the protein toward its final destination.

A protein structure is subject to a wide variety of chemical forces and influences. Some of its amino acids have an oily side which means they want to huddle together, shielded from the aqueous environment. Other amino acids fit well with water and so have no such repulsion from the environment. Some amino acids are charged, so they mutually attract or repulse each other. And some amino acids have sulfur atoms which can bond together.

These various influences help to guide the unfolded protein to its final shape. They overcome the entropy barrier, but just barely. The result is a folded protein that is marginally stable, which means they wiggle and shake a bit—a good thing for many protein functions. The marginal stability of proteins also helps when it comes time to take them apart. Proteins are temporary wonders. They are created for a need, and just as quickly torn down.

Kicking the paradox down the road

So the paradox is resolved. Proteins overcome their enormous entropy barrier with their various chemical interactions, as determined by their particular amino acids. In fact, just as the words on this page determine the message, so too the amino acid sequence determines the particular characteristics of a protein.

The vast majority of amino acid sequences one could dream up don’t work. Most won’t successfully fold up, and most of those that do result in a structure that is too stable. And most don’t result in any meaningful protein function. As discussed here, useful amino acid sequences are rare.

So while the protein folding paradox is resolved, there is a nagging feeling. Yes, the protein overcomes its entropy barrier—it all works just fine. But it works just fine only because a very special amino acid sequence was specified. That amino acid sequence is just as astronomically rare as the three dimensional structure that the unfolded protein was able to find. So from where did this amino acid sequence come?

The string of amino acids that make up a protein comes from the cell’s translating machine called the ribosome. The ribosome takes as input a string of nucleotides and produces as output a string of amino acids. The translation is done according to the genetic code.

And from where did the string of nucleotides come? It came from the DNA. A massive protein copying machine slides along an opened section of DNA and copies a gene.

And from where did the DNA gene come? According to evolution it evolved, but it is here that we find another entropy barrier. Just as the folding protein is confronted with an astronomical number of structures, so too the DNA gene is confronted with its own nightmare of choices. But that is where the similarities end.

A different kind of entropy barrier

A typical gene has something like a thousand nucleotides. Given that there are four different types of nucleotides, this means there are 4^1000 different sequences that could make up the gene. This is equal to a 1 followed by about 600 zeros—a big number. That’s more than the number of nano seconds since the Big Bang—by about 10^574 (a 1 followed by 574 zeros).

Finding the right gene sequence to get a particular job done in the cell would make finding a needle in a haystack seem easy. The problem is so difficult that we haven’t yet figured out the answer, but it would be a 1 in 10^100++ long shot. Do not try this at home.

It is a huge entropy barrier, but it has some important differences compared to the protein folding entropy barrier we saw above. First, this gene entropy barrier is due to the large number of possible DNA nucleotide sequences whereas the protein folding entropy barrier was due to the large number of possible protein shapes.

And the protein folding entropy barrier was overcome by those fortuitously coordinated chemical interactions, which as we saw traced back to the amino acid sequence, which in turn traced back to the gene sequence.

But the gene entropy barrier has no such convenient explanation. Genes don’t come together via prearranged, specified information to overcome all odds.

In fact evolution’s proposal is that genes first arise via some sort of random change mechanisms, such as mutations. Nucleotides somehow come together, somehow provide some function, somehow are able to replicate, somehow vary, and somehow find new gene sequences against the astronomical entropy barrier.

Implications for evolution

The fact that evolutionists do not have all the answers or details does not mean it did not happen, or is impossible. But it is a significant problem. Evolution is hardly the sort of idea one would call a fact. Unless one were an evolutionist, that is.

Evolutionists say evolution is a fact, and that all the evidence lines up behind the theory. There are no serious problems or issues. Only minor details to be worked out. Consequently for them this gene entropy barrier is no big deal. In fact, amazingly they argue it is not a problem at all.

This is another unfortunate example of how evolution corrupts science. In the hands of evolutionists, science is manipulated in strange ways to support their theory. In the case of this gene entropy barrier, evolutionists such as Ard Louis argue that the fact that since biology operates successfully everyday inspite of tremendous entropy barriers such as in the protein folding case, that therefore entropy barriers are really no problem for evolution either.

But as one can see from the protein folding and gene example discussed above, this argument makes no sense. As we saw, proteins overcome their entropy barrier via the many fortuitous chemical interactions that arise as a consequence of the very special amino acid sequence specified by the DNA gene.

The protein successfully folded because it was setup to fold. The scientist cannot then conclude that since this worked out so nicely that the origin of the gene itself (responsible for the special amino acid sequence) has no serious entropy challenge. They are two very different problems. The fact that the protein folds does not mean the gene evolves.

This argument that biology’s everyday overcoming of entropy shows that evolution can do the same thing (somehow), is simply a corruption of science. It is an unfortunate, yet common example of what evolution has done to our thinking. Religion drives science, and it matters.

92 comments:

In the case of this gene entropy barrier, evolutionists such as Ard Louis argue that the fact that since biology operates successfully everyday inspite of tremendous entropy barriers such as in the protein folding case, that therefore entropy barriers are really no problem for evolution either.

I think that is not a fair representation of Ard Louis’ argument. As I said on the referenced thread, his argument was that “If one can accept that life operates according to natural law, it follows that one’s mind may be open to the proposition that the history of life operated according to natural law.”

We all agree that the origin of life is an unsolved scientific problem, just as there are innumerable unsolved scientific problems in other fields.

I think in general it would be more constructive if Dr Hunter would represent the views of scientists more objectively. Portraying scientists as foolish and/or duplicitous is a cheap rhetorical gambit and an ad hominem fallacy to boot.

"I think that is not a fair representation of Ard Louis’ argument."=====

Not at all. Ard Louis is a Theistic Evolutionists. Yet in his arguements, he takes up a position of an Atheistic Evolutionists and never ONCE explains(TE shills never do) how their god Jesus got the ball rolling and covered the bases with regard all those evil obstacle barriers that Atheism's version can't answer. He therefore puts himself on the side of all the other blind-faithers.------

Pedant:

"We all agree that the origin of life is an unsolved scientific problem, . . "=====

It is after all the Atheist Virgin Birth Story.

Evolutionists Shapiro and Yockey at least have the testosterone to actually bodly say it is "unsolvable" and "unknowable" and leave the story telling on this point to the Shammn Philosophers among this world's corrupt elite.

Now to be fair, though someone who believe and has faith in creation may believe in a creator, it is still the same identical challenge for them to prove the same step by step criteria for a scientific naturalistic explanation ONLY on any research paper just how they THINK their god did it. I would say this is impossible in the perfect sense, since no of them were actually present when they believe God accomplished this. Certainly time machines haven't been invented yet, with the exception of HG Wells wild science fictionary imagination. The main possitive on their side is the human experience with regards the designing of complex things(for which we all can relate) we are all familiar with, it's hard for most intelligent persons to grasp blind pointless indifference accomplishing anything remotely revealing the actual precision and sophitication we observe in nature. That's why at best when it comes to naturalistic explanations, we only have 100% inference that life was designed and 0% inference that blind forces did it. Romans 1:20------

Pedant:

" . . just as there are innumerable unsolved scientific problems in other fields."======

There's actually no comparison to other scientific fields because other fields and those scientists involved in them are not pimping an unproven scam with lack of evidence, and promoting it through politicing, ideology and religious philosophy comfirmation classes. There's a huge GAP between evolution and other scientific fields.------

Pedant:

"I think in general it would be more constructive if Dr Hunter would represent the views of scientists more objectively. Portraying scientists as foolish and/or duplicitous is a cheap rhetorical gambit and an ad hominem fallacy to boot."=======

He doesn't have to make them look foolish, they do it to themselves. As another common quote of his, "You just can't make this stuff up." The fact that he openly exposes the load in their unterhosen for all the public to see I can understand is disturbing to your worldview and that is what this whole mess is about as you boldly stated once before. But I guess that was a slip.

It looks like my comment has disappeared into the void. Here is a Cliff-notes version of it.

4^1000 is the number of microstates of the system. Since entropy is the logarithm of the number of microstates, the entropy barrier in this case is log(4^1000) = 2000 log(2) = 1386. That's not particularly impressive. Simple physical systems are routinely able to penetrate such barriers.

An example of that would be an Ising magnet with N = 2000 spins. The number of microstates in the system is 2^N, say as in your example. Yet if you place this magnet in a low-temperature environment, it finds its ground states quickly. The number of states required for that is not 2^N but rather of order N, thanks to the feedback from the environment that takes place in the form of energy exchange. In fact, in this case free energy F = ETS rewards entropy reduction, so the system slides toward one of its ground states.

So remember this, Cornelius. Entropy is the logarithm of the number of microstates. Your astronomical numbers are not all that impressive. A simple magnet can beat them.

Instead of us just looking at the probability of finding a single ‘simple’ protein molecule by chance, (a solar system full of blind men solving the Rubik’s Cube simultaneou...sly (Hoyle), let’s also look at the complexity which goes into crafting the shape of just one protein molecule. Complexity will give us a better indication if a protein molecule is indeed the handi-work of an infinitely powerful Creator.

In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, which was 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it was estimated to take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape.

“Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000http://www.news.com/2100-1001-233954.html

Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule:

A Few Hundred Thousand Computers vs. A Single Protein Molecule – videohttp://www.metacafe.com/watch/4018233

As well, despite some very optimistic claims, it seems future ‘quantum computers’ will not fair much better in finding functional proteins in sequence space than even a idealized ‘material’ supercomputer of today can do:

The Limits of Quantum Computers – March 2008Excerpt: “Quantum computers would be exceptionally fast at a few specific tasks, but it appears that for most problems they would outclass today’s computers only modestly. This realization may lead to a new fundamental physical principle”http://www.scientificamerican.com/article.cfm?id=the-limits-of-quantum-computers

The Limits of Quantum Computers – Scott Aaronson – 2007Excerpt: In the popular imagination, quantum computers would be almost magical devices, able to “solve impossible problems in an instant” by trying exponentially many solutions in parallel. In this talk, I’ll describe four results in quantum computing theory that directly challenge this view.,,, Second I’ll show that in the “black box” or “oracle” model that we know how to analyze, quantum computers could not solve NP-complete problems in polynomial time, even with the help of nonuniform “quantum advice states”,,,http://www.springerlink.com/content/0662222330115207/

Here is Scott Aaronson’s blog in which refutes recent claims that P=NP (Of note: if P were found to equal NP, then a million dollar prize would be awarded to the mathematician who provided the proof that NP problems could be solved in polynomial time):

Shtetl-OptimizedExcerpt: Quantum computers are not known to be able to solve NP-complete problems in polynomial time.http://scottaaronson.com/blog/?p=456

Protein folding is found to be a ‘intractable NP-complete problem’ by several different methods. Thus protein folding will not be able to take advantage of any advances in speed that quantum computation may offer to any other problems of computation that may be solved in polynomial time:

Another factor severely complicating man’s ability to properly mimic protein folding is that, much contrary to evolutionary thought, many proteins fold differently in different ‘molecular’ situations:

The Gene Myth, Part II – August 2010Excerpt: the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html

Also of interest to the extreme difficultly man has in computing the folding of a protein within any reasonable amount of time, it seems water itself, (H2O), was ‘designed’ with protein folding in mind:

Protein Folding: One Picture Per Millisecond Illuminates The Process – 2008Excerpt: The RUB-chemists initiated the folding process and then monitored the course of events. It turned out that within less than ten milliseconds, the motions of the water network were altered as well as the protein itself being restructured. “These two processes practically take place simultaneously“, Prof. Havenith-Newen states, “they are strongly correlated.“ These observations support the yet controversial suggestion that water plays a fundamental role in protein folding, and thus in protein function, and does not stay passive.http://www.sciencedaily.com/releases/2008/08/080805075610.htm

Water Is ‘Designer Fluid’ That Helps Proteins Change Shape – 2008Excerpt: “When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life.”http://www.sciencedaily.com/releases/2008/08/080806113314.htm

,,,, As Frank Turek would say, ‘I Don’t Have Enough Faith To Be An Atheist’

The Pharisee stood and prayed thus with himself, God, I thank thee, that I am not as other men are, extortioners, unjust, adulterers, or even as this publican (Tax Collector)."=====

Another beautiful example of quote mining and leaving out the context when it exposes one's ignorance. LOL

Verses 13 & 14 of Luke 18:11-14 (Amplified Bible)

13) "But the tax collector, [merely] standing at a distance, would not even lift up his eyes to heaven, but kept striking his breast, saying, O God, be favorable (be gracious, be merciful) to me, the [b]especially wicked sinner that I am!"

13) "I tell you, this man went down to his home justified (forgiven and made upright and in right standing with God), rather than the other man; for everyone who exalts himself will be humbled, but he who humbles himself will be exalted."

How Proteins Evolved - Cornelius Hunter - December 2010Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.http://www.uncommondescent.com/intelligent-design/how-proteins-evolved/

But you knew that Zach, thus why the blatant dishonesty acting as if 1 in10^12 is of any use to you whatsoever for the Darwinian framework??? Is it more important for you to unsuccessfully try to deceive others than to be honest with yourself?

The question about the origin of life is very closely related to how life evolves. Claiming that we know that complex lifeforms evolved by random mutations and natural selection is of course a big lie, and its pretty much as unlikely as life originating from random processes in the first place.

Nobody is not claiming scientists are foolish or gullible, but many people would say that evolutionists are. Its the evolutionists who claim that belief in the theory of evolution is "science". True, many "scientists" do belive in the theory, but there are probably a lot more "scientists" who question it.

Sorry Bunky. According to polls over 90% of all scientists, and over 99.5% of scientists in the life sciences (biology, genetics) accept the ToE. So you'll have to come up with a different hand wave.

And claiming the theory is a proven fact has of course nothing to do with science wahtsoever...

CH and his goofy IDCer minions are the only ones confusing the observed fact of evolution with the theory of evolution. Are you that dense too?

So most proteins don't actually fold on their own. Lots of things facilitate the folding of proteins... like one of the main functions of the rough endoplasmic reticulum is to fold proteins, also other proteins can aid in folding proteins. This is something you could learn in a high school biology course. There are four different levels of protein structure 1)Primary - the polypeptide chain, 2)Secondary - (a) helices or (b) sheets, 3)Tertiary - regions of secondary structure and randomly coiled regions fold into a three-dimensional conformation , and 4)Quaternary - Two or more polypeptides may associate with each other.

So which one of these levels of protein structure folding does the 1*10^100+++ probability apply to? And also did you include the folding aids into your calculation? Minor correction in your article an amino acid chain falls into the category of primary structure which would make it a polypeptide chain.... not a protein... only after the polypeptide chain is folded does it become a protein and most proteins exist at the quaternary structure level.

If your curious where all this information comes from... I'm a BS Biology undergrad studying at Augusta State University and this is in our genetics text book; however, you could also probably find all this info in a basic biology high school text book post 1995. Just saying maybe you should do a little more research before posting some ridiculous article.

The textbook is Genetics Analysis and Principles 3rd Ed. Booker, Robert J.

bornagain77: Instead of us just looking at the probability of finding a single ‘simple’ protein molecule by chance, (a solar system full of blind men solving the Rubik’s Cube simultaneou...sly

Zachriel: Actually, let's look. It's more likely than 10^-12.

bornagain77: And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier.

A few billionths of a gram of protein sequences.

bornagain77: But you knew that Zach, thus why the blatant dishonesty acting as if 1 in 10^12 is of any use to you whatsoever for the Darwinian framework???

It was *you* who suggested that the probability of finding a single ‘simple’ protein molecule by chance was implausible, on the order of a "solar system full of blind men solving the Rubik’s Cube". That is incorrect.

So true, and I will admit you have a 1 in a trillion functional protein as soon as you show me a randomly generated protein that is actually functional (i.e. actually does something useful) instead of just 'gumming up' the works:

A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial CellsExcerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division."http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385

bornagain77: So true, and I will admit you have a 1 in a trillion functional protein as soon as you show me a randomly generated protein that is actually functional (i.e. actually does something useful) instead of just 'gumming up' the works:

In other words, you will only admit your error when some other argument is made. This is your original claim:

bornagain77: Instead of us just looking at the probability of finding a single ‘simple’ protein molecule by chance, (a solar system full of blind men solving the Rubik’s Cube simultaneou...sly

That claim was simply false. Instead of admitting your error, and perhaps even learning something, you continue with this:

bornagain77: But you knew that Zach, thus why the blatant dishonesty acting as if 1 in 10^12 is of any use to you whatsoever for the Darwinian framework???

Human Gene Count Tumbles Again – 2008Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes.,,, Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primategenomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. (The 1,177 ORFan genes in humans are completly unique to our lineage)http://www.sciencedaily.com/releases/2008/01/080113161406.htm

In fact it turns out that the authors of the preceding ‘kick the ORFans out in the street’ paper actually did know that there was clear and unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore that strong evidence in favor of their preconceived evolutionary bias of forcing the genetic sequences of chimps and humans to be as similar as possible. That is EXACTLY how you ARE NOT suppose to practice science!!!:http://www.uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358547

New ORFan genes are found to be just as essential as older genes:

Age doesn't matter: New genes are as essential as ancient ones - December 2010Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."http://www.sciencedaily.com/releases/2010/12/101216142523.htm

My my, we're back to the big numbers game again. Interestingly, with even weaker empirical data, we've gained another 474 zeros from Hunter's last estimates.

Just to be clear, Entropy is the driving force in protein folding. Hydrophobic (oil-like) residues do not interact (bond) with water. This causes water to organize (cage) around them-a massive entropic penalty. The packing of hydrophobic residues into a protein core allows water to disorganize. So the entropy of water drives protein folding, despite the conformational entropy of the amino acid side chains.

This has a very important influence in the numbers game. Since only about 1/3 of residues are in a core, the 'search' for a fold in sequence space isn't 20^n, where n is the number of residues in a protein. It would be 20^n/3. We could go even further, and use the similarity of hydrophobic residues to argue most could substitute in the core. Perhaps we'd be reduced to 6^n/3 or even 2^n/3, for a simple hydrophobic/hydrophilic binary code. Much smaller numbers.

This again, completely ignores that evolution didn't have to hit a certain fold, and likely proceeded through sub-folds, simple zinc fingers or bundles, But regardless, well thought out estimates of achieving a lysozyme fold only peg it at 1 in 10^10 (Dill 1990/1991, see below).

The rest is just degeneracy-an well observed feature of sequence space, that many, many sequences can yield the same fold.

References:Lau KF, Dill KA. 1990. Theory for protein mutability and biogenesis. Proc Natl Acad Sci USA 87 :638– 642. "The simulations also show that (i) the number of "convergent" sequences (different sequences coding for the same native structure) is extremely large and (ii) most sequences become quite dense under folding conditions. This implies that the probability of formation of a globular protein from a random sequence of amino acids by prebiotic or mutational methods is significantly greater than zero."

Chan HS, Dill KA. 1991. “Sequence space soup” of protein and copolymers. Journal of Chemical Physics, Vol. 95, No. 5. 3775-3787. "In these respects, this simple model shows that proteinlike behavior should arise simply in copolymers in which one monomer type is highly solvent averse. It suggests that the structures and uniquenesses of native proteins are not consequences of having 20 different monomer types, or of unique properties of amino acid monomers with regard to special packing or interactions, and thus that simple copolymers might be designable to collapse to proteinlike structures and properties."

"Substitutions of solvent-exposed amino acids on the surfaces of proteins are seen to have little if any effect on protein stability or structure, leading to the view that it is the rigid parts of proteins that are critical for folding and stability."

A simple library of random sequences composed of glutamine, leucine and arginine are helical and display a variety of native-like properties. Despite Hunter's objections, many show cooperative folding, and not all are overly stable*. Some have stabilities of that of some average proteins.

(*Whatever that means: very stable proteins are found in you and I- gamma-D-crystalline and nucleosomes melt around 75 Celsius. A few zinc fingers I can think of are stable to nearly 100 Celsius. E. coli ribosomes melt from 45-85. So marginal stability is normal, but not a requirement for all proteins).

===4^1000 is the number of microstates of the system. Since entropy is the logarithm of the number of microstates, the entropy barrier in this case is log(4^1000) = 2000 log(2) = 1386. That's not particularly impressive. Simple physical systems are routinely able to penetrate such barriers. ===

You will be glad to hear the entropy barrier is much less than 1386 nats due to degeneracies. Let's conservatively call it 500 bits just to have a nice round number. And what does this mean. It means that finding a good gene sequence is about a one out of 2^500, or one out of 10^150, (or a 1 followed by 150 zeros) long shot.

In statistical mechanics and information theory entropy is the logarithm of the number of microstates, or number of messages, respectively. Using log base 2, the entropy then gives you the number of bits required to enumerate the sequences. One bit gives you two sequences, two bits give you 4 sequences (2^2), 8 bits give you 256 sequences (2^8), and so forth. 500 bits give you 10^150 sequences.

===So remember this, Cornelius. Entropy is the logarithm of the number of microstates. Your astronomical numbers are not all that impressive. ...===

The gene entropy barrier may be expressed as the entropy (log of the number of sequences to search through), or simply as the number of sequences. For our purposes the latter is more appropriate simply because evolution must construct the actual sequences (which then may be selected for, or not). Evolution does not search through 500 bits, it searches through 10^150 sequences.

===An example of that would be an Ising magnet with N = 2000 spins. The number of microstates in the system is 2^N, say as in your example. Yet if you place this magnet in a low-temperature environment, it finds its ground states quickly. The number of states required for that is not 2^N but rather of order N, thanks to the feedback from the environment that takes place in the form of energy exchange. In fact, in this case free energy F = E-TS rewards entropy reduction, so the system slides toward one of its ground states.

So remember this, Cornelius. Entropy is the logarithm of the number of microstates. Your astronomical numbers are not all that impressive. A simple magnet can beat them. ====

This is another example of how evolution corrupts and mocks science. If evolution were not at stake evolutionists would never make these absurd arguments. Here, the professor proposes a "simple magnet" as a useful analogy to evolution finding good genes. He is far too smart for this, but that's evolution for you. The analogy is not even wrong, it is completely out to lunch. Yes, a simple magnet easily defeats big entropy barriers. And that is completely irrelevant to the problem of evolution finding good genes.

This argument parallels the evolutionary argument we have been looking at. That is, because biological processes routinely defeat big entropy barriers, therefore evolution ought to be able to as well. The professor could just as easily have used protein folding as his example. Proteins also defeat big entropy barriers when they fold to their native conformation. So what?

And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist

The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,

‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,

Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,

,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA

“The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology

This following video and article are much more clear for explaining exactly why mutations to the DNA do not control Body Plan morphogenesis, since the mutations are the ‘bottom rung of the ladder’ as far as the 'higher levels of the layered information’ of the cell are concerned:

You will be glad to hear the entropy barrier is much less than 1386 nats due to degeneracies. Let's conservatively call it 500 bits just to have a nice round number. And what does this mean. It means that finding a good gene sequence is about a one out of 2^500, or one out of 10^150, (or a 1 followed by 150 zeros) long shot.

Only if you make the ridiculous assumption that all the parts had to spontaneously self-assemble all at once, something that no competent scientist anywhere accepts as reality. Do you think you'll ever be bright enough to understand that you can't calculate the probabilities of a long term iterative process by taking a one time snapshot of the results? I don't think your severe religious biases will let you.

The gene entropy barrier may be expressed as the entropy (log of the number of sequences to search through), or simply as the number of sequences. For our purposes the latter is more appropriate simply because evolution must construct the actual sequences (which then may be selected for, or not). Evolution does not search through 500 bits, it searches through 10^150 sequences.

No it doesn't, and it doesn't have to. It only searches through the variants present in each generation, keeps the ones that work and uses them (with small modifications) for the next generation. This iterative process of selection and filtering has been going on for over 3 billion years.

Really CH, your "argument from big probabilities" is about as stupid as they come. Even your fellow IDiots and Creationists like AIG have abandoned it. Did you not get the memo?

Only if you make the ridiculous assumption that all the parts had to spontaneously self-assemble all at once, something that no competent scientist anywhere accepts as reality. Do you think you'll ever be bright enough to understand that you can't calculate the probabilities of a long term iterative process by taking a one time snapshot of the results? I don't think your severe religious biases will let you.

The gene entropy barrier may be expressed as the entropy (log of the number of sequences to search through), or simply as the number of sequences. For our purposes the latter is more appropriate simply because evolution must construct the actual sequences (which then may be selected for, or not). Evolution does not search through 500 bits, it searches through 10^150 sequences.

No it doesn't, and it doesn't have to. It only searches through the variants present in each generation, keeps the ones that work and uses them (with small modifications) for the next generation. This iterative process of selection and filtering has been going on for over 3 billion years.

Unfortunately this is the sort of bad math and worse science lately seen in evolutionism since the glittering contributions of philosophers such as CDawkins and his Weasel Generator. Worse, it is the ready resort to Teleology. Yes, the math is against us. But evolutionism is the best theory of origins, to date. And we must go with it.

My math is rustier than Bill Occam's razor, but I think that both sides sometimes mischaracterize some probabilities. For any event that is known, that has happened, then the probability now is unity, certainty or 1. If I were to drop a glass jar on the floor and it shatters in all directions, the advance probability that all the tiny pieces would lay out "just so" is extremely improbable. But, once the glass jar has shattered on the floor and we now see the layout of the pieces, then the probability is one, unity, certainty. For very high improbabilities, lately, I see evolutionists who either fail to see the math, or believe they can make an availing argument by producing ever more multipliers out of thin air (bad philosophy). What..you say it could not happen on earth...well we now are assured there must be a quadrillion other earths out there? That's still not enough of a multiplier? Well we can be assured there must be a billion other...parallel universes. Still doesn't lower the odds? Well, then there must be a trillion other dimensions we don't know about yet.

Unfortunately this is the sort of bad math and worse science lately seen in evolutionism since the glittering contributions of philosophers such as CDawkins and his Weasel Generator. Worse, it is the ready resort to Teleology. Yes, the math is against us. But evolutionism is the best theory of origins, to date. And we must go with it.

You mean the Weasel program that you totally misunderstood the purpose and operation of.

My math is rustier than Bill Occam's razor, but I think that both sides sometimes mischaracterize some probabilities. For any event that is known, that has happened, then the probability now is unity, certainty or 1. If I were to drop a glass jar on the floor and it shatters in all directions, the advance probability that all the tiny pieces would lay out "just so" is extremely improbable. But, once the glass jar has shattered on the floor and we now see the layout of the pieces, then the probability is one, unity, certainty.

That means when some IDiot after the fact says "the probability of the glass shards falling exactly that way was 10^150, so it's too improbable that that glass jar fell. The glass shards must have been intelligently placed that way!" you'll know to laugh at him. Right?

For very high improbabilities, lately, I see evolutionists who either fail to see the math, or believe they can make an availing argument by producing ever more multipliers out of thin air (bad philosophy).

Show us the "very high improbabilities". Show us the calculations, and justify any assumptions you make. Explain how the "math is against us", and how "multipliers came out of thin air". CH sure can't.

So far you haven't exhibited the slightest understanding of evolutionary theory. Do you have some sort of point?

Only if you make the ridiculous assumption that all the parts had to spontaneously self-assemble all at once, something that no competent scientist anywhere accepts as reality. Do you think you'll ever be bright enough to understand that you can't calculate the probabilities of a long term iterative process by taking a one time snapshot of the results.

This point has to be emphasized every time a Creationist makes a probability argument about the possible origin of a biological structure . It is not possible to calculate the probability of a past event without knowing the history of that event. Taking today's hemoglobin as an example, nobody, including Cornelius Hunter, knows its complete history through geological time. So when he advances such arguments, he is talking nonsense.

This is a prime example of how Creationism corrupts and mocks science. If their religious beliefs were not at stake, Creationists would never make such arguments. Hunter is far too smart for this, but that's Creationism for you. His calculation is not even wrong, it is completely out to lunch. Yes, his simple-minded entropy calculation easily defeats evolutionary theory. But it is scientifically useless.

bornagain77: So Zach let's just see how honest you are, does one in a trillion functional proteins help you in a Darwinian scenario?

So bornagain77, let's just see how honest you are. You made a significant misstatement. You reply by casting aspersions and rendering a dozen irrelevant quotes. Is there a reason why you keep diverting?

bornagain77: Instead of us just looking at the probability of finding a single ‘simple’ protein molecule by chance, (a solar system full of blind men solving the Rubik’s Cube simultaneou...sly

That was a false statement. You should admit the error, and perhaps try to learn why you were mistaken on such an important aspect of the discussion.

Zachriel: That was a false statement. You should admit the error, and perhaps try to learn why you were mistaken on such an important aspect of the discussion.

I'm pretty sure he was talking about a protein like the types we find operating in cells, not something that simply binds to ATP like the study you mentioned. Forming simple ligands is much easier than performing a critical, selectable role in a cellular context. I think his original intentions are confirmed by the fact that he illustrated what happened when those proteins were placed in a cellular environment. He does not seem to be guilty of moving the goalposts to me.

John: I'm pretty sure he was talking about a protein like the types we find operating in cells, not something that simply binds to ATP like the study you mentioned.

That's fine, but that's not what he said, which concerned a single ‘simple’ protein molecule.

John: Forming simple ligands is much easier than performing a critical, selectable role in a cellular context.

Sure. Then he should restate his claim rather than resort to accusations and indirection. Once he had done so, we would have been happy to engage on what this means for evolutionary biology.

John: I think his original intentions are confirmed by the fact that he illustrated what happened when those proteins were placed in a cellular environment.

It wasn't clear whether such a protein would maintain its function inside a living cell. Putting the synthetic ATP binder in a cellular context demonstrated that the ATP was not only functional, but functionally specific. From bornagain77's cite:

Stomel et al., A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells, PLoS ONE 2009: Based on the data collected, we suggest that the function of DX as an ATP-binding protein is responsible for disrupting the energetic balance within the cell. Several lines of evidence indicate that DX remains folded when expressed in E. coli.

This particular protein differs from the natural ligands, indicating many possible solutions to the same functional problem. Furthermore, the authors suggest that there may be therapeutic potential for such proteins.

Taking today's hemoglobin as an example, nobody, including Cornelius Hunter, knows its complete history through geological time. So when he advances such arguments, he is

-It should be simple ,somebody should know. Gentleman posted few weeks ago- replicator is just replicator. Bam! See,so simple.

Rhod

No it doesn't, and it doesn't have to. It only searches through the variants present in each generation, keeps the ones that work and uses them

--

Who or what does this searching, Rhod. How this search happens? Please help me visualize this process of search and selection in a soup of random amino acids. These are big molecules, chunks of matter. We should be able to visualize them. It's not like trying to visualize electron, photon or other quantum unit. There is nothing to visualize there. Just mathematics.

"No it doesn't, and it doesn't have to. It only searches through the variants present in each generation, keeps the ones that work and uses them"

Who or what does this searching, Rhod. How this search happens? Please help me visualize this process of search and selection in a soup of random amino acids. These are big molecules, chunks of matter. We should be able to visualize them. It's not like trying to visualize electron, photon or other quantum unit. There is nothing to visualize there. Just mathematics.

That was my comment, not Rhod's.

"Search" is a metaphorical term for the process of natural selection, i.e. differential reproductive success. There is no intelligent entity doing active searching.

Evolution "searches" for the variants that provide the highest reproductive fitness the same way a sieve "searches" for small particles to let through while filtering out larger ones.

As Zachriel already answered, the spontaneous formation of some of the precursor complex organic molecules required for life from the basic elements. Evolution doesn't kick in until you get the first imperfectly self-replicating molecules undergoing differential selection. How we got from the precursor molecules to the first self-replicators is what the science of abiogenesis is investigating.

This point has to be emphasized every time a Creationist makes a probability argument about the possible origin of a biological structure .

It seems like the tornado-in-the-junkyard argument is still going strong. Interesting, isn't it, that when some people claim to offer arguments against evolution, they often argue against a pure chance hypothesis.

It is not possible to calculate the probability of a past event without knowing the history of that event.

Perhaps Cornelius thinks that the very claim that there actually is a history is a metaphysical one.

I still don't understand Ard Louis argument. Is he really comparing the way that proteins fold into the same shape consistently to the way evolution will find the "right" solution given enough time? Is he comparing brownian motion and protein stability to random mutation and natural selection?

That seems like a horrifyingly misguided argument. I wouldn't imagine that most evolutionists think this way.

===I still don't understand Ard Louis argument. Is he really comparing the way that proteins fold into the same shape consistently to the way evolution will find the "right" solution given enough time? Is he comparing brownian motion and protein stability to random mutation and natural selection?===

Yes, but he is coming at it from a different angle. He says using ID reasoning, we would conclude that protein machines such as the flagellum are so complex that they could not have self-assembled. Since we know this is a false conclusion, we ought to steer clear of this type of reasoning for the origin of complexity. Put that way, it can seem like a good argument. But only if you don't think about if very hard.

===That seems like a horrifyingly misguided argument.===

Yes, agreed.

===I wouldn't imagine that most evolutionists think this way. ===

Well I would say yes and no. Certainly evolutionists (and evolutionists who should know better) have vigorously defended the argument.

As I pointed out it does parallel Descartes argument for naturalism. And while neither Descartes or Louis versions of this argument are prominent in the evolutionary literature, these arguments do fall into the broader category of philosophical arguments for naturalism, which is rampant in the literature.

In fact evolutionists simultaneously claim that (i) naturalism is a scientific fact and (ii) naturalism is required for legitimate scientific theories. Such serendipity.

Isn't it more the case that naturalism is required for successful scientific theories? In other words ones that provide a workable explanatory framework (but not necessarily complete) and often have practical out workings? (last time I checked alchemy has not actually proven to be of much use on either count).

Again CH if you want to make a case for a non-naturalistic scientific theory, you're going to have to make the case for it and provide a solid and workable framework. Instead you seem to want to focus on "Phase 1 - the Problem", rather than move to "Phase 2 - possible solutions". Which of course is why this blog feels like it is a stuck record saying the same old thing over and over (you could probably recycle old entries from a year ago and nobody would even notice...)

But so far there seems little indication that you are your ID cohorts are making much progress on these lines ( a quick look at www.biologic.com shows remarkably little work done in 5 years, but I guess at least they are trying). Which of course begs the question - why are non-naturalistic explanations & theories so darn elusive and hard to pin down? If there is an intelligent agency behind all this, that agency certainly isn't interested in communicating!

And of course if you do it would be a remarkable achievement that would completely revolutionize science - I daresay worthy of a Noble prize even.

Er...no thanks. I don't bat from that side of the plate. Try Eocene or Gary.

Perhaps you have misconstrued the anatomy to which the oafish troll was referring... :)"=====

Interesting to see that perverted decadant minds think alike. This is what happens when there's nothing of import and real worth to discuss any longer. Not that there necessarily was before. It's almost like a loop hole thingy so that Cornelius won't delete the obvious rules infraction.

They don't like to talk about soup, salad, and appetizers. They jump to what they consider meat and potatoes and claim masterchef. The problem is they've never once graduated from Jack-In-The-Box burger flipping school and moving on to receive a Wolfgang Puck's gourmet university diploma. In their minds, this excuses them from ever having to prove how unguidance, undirectedness, blind indifference without purpose or intent accomplished anything remotely intelligent. If they actually were forced to do this, they'd look like the fools they are and that would prevent them from actually debating what they really want to debate. What's that ??? The evils of some news pundit in your country called Bill O'Reilly, the wickedness of a George Bush, the insightful brilliance of Michael Moore, etc, etc, etc.

Surely you didn't think this was about science did you ??? *eyes rolling*

Cornelius Hunter: In fact evolutionists simultaneously claim that (i) naturalism is a scientific fact and (ii) naturalism is required for legitimate scientific theories.

Not sure who these so-called evolutionists are, but the distinction between natural and supernatural isn't always well-defined. When the supernatural refers to traditional actors, e.g. demons and spirits, scientists have found such entities to lack explanatory utility; and other explanations for many phenomena once attributed to spirits (disease, planetary movements, tilting picture frames, etc.) have been found sufficient, and the spirits scientifically superfluous. Some scientists might even say that the supernatural — as so-defined — has been debunked.

Most scientists use naturalism as a kind of heuristic, i.e. methodological naturalism. Sign on Chemistry Lab Door: NO DEMONS BEYOND THIS POINT.

However, naturalism in its broadest sense is a metaphysical position. We wouldn't want to conflate the various senses of the word, though.

natschuster: And what helps the heat shock proteins maintain their shape?

This is like asking what keeps diamonds in shape under the high pressures of the mantle. Not all proteins are of equal stability. If HSPs were not competently internally bonded, they would be of little use in maintaining other proteins.

If your line of reasoning resulted in any kind of possibly conceivable chicken-and-egg problem, it would have been on thousands of creationist websites by now.

To quote Jonathan Sarfati: "Life presents us with many such ‘chicken-and-egg’ problems for which naturalistic theorists have no answer. Creationists do have an answer—in the beginning, God created a fully functional chicken, which then laid an egg. Problem solved!"

The Biblical account of Samson says that in one day Samson slew a thousand Philistines with the jawbone of an ass. Every day millions of arguements for evolution by evolutionists themselves are killed with the same weapon.

Acceptance of first life by a creator is not an argument from ignorance but from scientific knowledge of what nature is and isn't capable of doing. Natural processes by themselves have been shown to be grossly insufficient to organize the molecules to produce life. Evolutionists are in a state of eternal denial of these scientific findings. Their prejudice is clear because they're always pretending to be a simple step away from an explanation.

So some proteins don't need heat shock proteins. Okay. But then how did the proteins that do need heat shock proteins evolve? They couldn't evolve unless the HSP already existed. But the HSP wouldn't evolve because they weren't needed yet.

And, while I'm prepared to admit my ignorance, along with numerous other defects, I don't think that a lack of self awareness is a problem I suffer from.

Neal Tedford:Acceptance of first life by a creator is not an argument from ignorance but from scientific knowledge of what nature is and isn't capable of doing. Natural processes by themselves have been shown to be grossly insufficient to organize the molecules to produce life.

"Grossly insufficient" is just your opinion. The only fact is that no one has ever recorded the emergence of entirely new life. Intelligence-guided processes have not been shown to produce life either... but I guess that doesn't matter to you.

Janfield:- Virgin births- Limbs spontaneously growing back- Men walking on water- People brought back from life- Talking donkeys- Floating wooden boxes (built by a handful of people) that contain the entire world's species

Oh, it's much worse than you describe. Here's a list to compare to each thing you listed -

I feel that the chances of the existence/occurrence of each thing on the right is much less likely than what you've listed on the left given the fundamental laws of nature. Some people find it hard to believe that limbs could grow back. Some people find it hard to believe that limbs could even exist. When confronted with evidence of the latter, the former seems a trivial admission.

Given my observation that Cornelius often takes quotes out of context to make his points, I went to the BioLogos Foundation and sought for the complete video by Ard Louis.

Ard's point is far from the misrepresentation portrayed by Cornelius. The point in the part showed by Cornelius was that it is risky to claim that something is impossible given perceived complexity (I would add to this misrepresented complexity, as he does with the problem of protein evolution). A previous point was that claiming something to be impossible because we don't know how it happens/happened puts ID at par with a god-of-the-gaps argument, most importantly because then where does ID get once science discovers natural paths or processes closing such gaps? (As it has happened many times already.)

I don't see how Cornelius would have missed the point other than on purpose. Which is what he obviously, and transparently did with my comments.

There are reasons why it is important to distinguish evolution from abiogenesis. Evolution is well understood, while abiogenesis is much more complicated. I am on the side that we might never know how life started on Earth exactly. But pretty sure that we will know it can happen in a number of ways, with no way of knowing which ones might have worked out our history.

Another reason is that evolution is quite easy to understand and undeniable once properly understood. Knowing the difference helps break misconceptions about it, and allows for explanations that can be understood by the more general public. By focusing on abiogenesis, or on detailed and misguided representations of what the problems for the evolution of something like a first protein, people who actually know better (such as the host of this blog), protect themselves from being shown wrong. This is why Cornelius won't ever attempt to try and answer my main question before: what is the thermodynamic barrier that appears when reproducing a selected subpopulation that does not appear when reproducing an established population. He rather went for an ad hominem. He knows that if we start here he will be shown to have nothing against evolution proper. Focusing on problems that are easy to misrepresent at many levels (such as protein evolution immersed into a misrepresented origin of life scenario) makes explanations very hard because we first have to work on the many misconceptions. A titanic task.

Unfortunately this is the sort of bad math and worse science lately seen in evolutionism since the glittering contributions of philosophers such as CDawkins and his Weasel Generator. Worse, it is the ready resort to Teleology.

Thornton said,You mean the Weasel program that you totally misunderstood the purpose and operation of.

Another person heard from who appears to endorse the lamentable, pop trend to smuggle Teleology into (what should be) science. It just makes evolution and all the hard work of men like CDarwin, DrHaeckel and company look very sad, when we see hucksters with "Weasel Generators".

My math is rustier than Bill Occam's razor, but I think that both sides sometimes mischaracterize some probabilities. For any event that is known, that has happened, then the probability now is unity, certainty or 1. If I were to drop a glass jar on the floor and it shatters in all directions, the advance probability that all the tiny pieces would lay out "just so" is extremely improbable. But, once the glass jar has shattered on the floor and we now see the layout of the pieces, then the probability is one, unity, certainty.

Thornton said,That means when some IDiot after the fact says "the probability of the glass shards falling exactly that way was 10^150, so it's too improbable that that glass jar fell. The glass shards must have been intelligently placed that way!" you'll know to laugh at him. Right?

As I said, can only wish that evolutionism would someday begin to attract a set of new folks with a firm grasp of hard science, math, probabilities. Instead, the almost diagnostic lack of math and probabilities is the norm. Thornton does see that forecasting a certain disposition (in this example: of the shattered pieces of glass) is very improbable. Suggests 10^150. But he fails to continue the analogy, and lack of probability, into the even more remote probability of reproducing that identical layout (of shattered glass pieces)..over and over again. The math is fatally against us evolutionists, at this time, and the hypercomplexity of these proteins is a daunting challenge to evolution sciences.

"As I said, can only wish that evolutionism would someday begin to attract a set of new folks with a firm grasp of hard science, math, probabilities."

Only someone completely unfamiliar with the science of evolutionary biology would make such a ridiculous claim, since anyone familiar with the field knows that thousands of mathematicians, engineers and physicists already work in evolutionary biology, and this has been so for decades.

"Only someone completely unfamiliar with the science of evolutionary biology would make such a ridiculous claim, since anyone familiar with the field knows that thousands of mathematicians, engineers and physicists already work in evolutionary biology, and this has been so for decades."=====

natschuster:So some proteins don't need heat shock proteins. Okay. But then how did the proteins that do need heat shock proteins evolve? They couldn't evolve unless the HSP already existed. But the HSP wouldn't evolve because they weren't needed yet.

Any proteins that are vitally dependent on HSPs could not have become so until after HSPs were present. That said, HSPs are in bacteria as well as humans; they are ancient proteins. Prior to HSPs, there are at least 2 possibilities: 1) life used a smaller set of proteins that did not require HSPs. 2) Some other protein or molecule filled the role of HSPs (but not as well, as HSP life survives whereas pre-HSP life does not).

New proteins first appear in cellular environments where they are not absolutely vital; however, their presence may confer an advantage (or at least no substantive disadvantage), and so they may be passed down to descendants. Proteins that don't require HSPs for survival generally would certainly benefit from them if an organism encountered an environment of heat stress (mid-ocean ridges and hot spots come to mind). Over time, the presence of HSPs allows a diversity of proteins to evolve that are utterly dependent upon them. Thus, what was a luxury is now a necessity.

A new paper just came out in Science on this very topic (proteins becoming essential due to interactions and arising functions, some in as "little" as 3 million years). A summary can be found here.

And, while I'm prepared to admit my ignorance, along with numerous other defects, I don't think that a lack of self awareness is a problem I suffer from.

Apologies if that seemed like an insult targeted at you. I put the lack of self-awareness remark right after the Sarfati quote that inspired it. However, now that you brought it up, if you did lack self-awareness, how would you know that you were lacking it?

"Life could never have arisen from non-living chemicals under any environmental conditions, because no new life arose in my jar of peanut butter last week."=====

I live in the frozen frigid north of Scandinavia. When I come home each day the living room is often a complete mess. Sometimes it happens while I'm present right before my very eyes and it's been suggested that woolly mammoths are doing this by running at Clark Kent(Smallville) super speeds through my house and that's why I don't see them. I've been told that just because I don't see them doing this doesn't mean they don't exist. (MAYA = ILLUSION)

I don't care what parallel universe you believe you are existing in right now, but I don't see the differences between any of your sides. This mess is NOT about science. It's about politics, ideology, philosophy and WORLDVIEW of all three sides. All three need to be eliminated soon if there is any hope of salvaging what's left of this planet. *wink*

"Luis Pasteur demostrates that life come from life. Did you find a falsification?"=====

They have something better. It's called modern day computer animation technology where any philosophical concept can come to life via the imaginative rigging by a good anonymous programmer who favours the right side of the worldview power struggle issue!!!

Another person heard from who appears to endorse the lamentable, pop trend to smuggle Teleology into (what should be) science. It just makes evolution and all the hard work of men like CDarwin, DrHaeckel and company look very sad, when we see hucksters with "Weasel Generators".

You still don't understand the the purpose and operation of the Weasel program I see.

As I said, can only wish that evolutionism would someday begin to attract a set of new folks with a firm grasp of hard science, math, probabilities. Instead, the almost diagnostic lack of math and probabilities is the norm.

You forgot to show us your probability calculations and assumptions for your claimed "very high improbabilities" of biological life. I guess that makes you even more ignorant than those evolutionary biologists and geneticists.

Thornton does see that forecasting a certain disposition (in this example: of the shattered pieces of glass) is very improbable. Suggests 10^150. But he fails to continue the analogy, and lack of probability, into the even more remote probability of reproducing that identical layout (of shattered glass pieces)..over and over again.

But DNA --> protein formation isn't random like glass shards. It follows know laws of chemistry and physics. Why should the same chemical reaction occurring under the same conditions not produce similar results each time?

The math is fatally against us evolutionists, at this time, and the hypercomplexity of these proteins is a daunting challenge to evolution sciences.

Who's "us"? Since you've demonstrated zero understanding of actual evolutionary theory or probability, you don't qualify as an evolutionist.

I live in the frozen frigid north of Scandinavia. When I come home each day the living room is often a complete mess. Sometimes it happens while I'm present right before my very eyes and it's been suggested that woolly mammoths are doing this by running at Clark Kent(Smallville) super speeds through my house and that's why I don't see them. I've been told that just because I don't see them doing this doesn't mean they don't exist. (MAYA = ILLUSION)

But DNA --> protein formation isn't random like glass shards. It follows know laws of chemistry and physics. Why should the same chemical reaction occurring under the same conditions not produce similar results each time?

Because evolution is random chaotic undirected stochastic chance!!!!! We know that random chaotic undirected stochastic chance would never produce a viable protein out of a random chaotic undirected stochastic chance soup of amino acids!!!!!

But DNA --> protein formation isn't random like glass shards. It follows known laws of chemistry and physics. Why should the same chemical reaction occurring under the same conditions not produce similar results each time?

Because evolution is random chaotic undirected stochastic chance!!!!! We know that random chaotic undirected stochastic chance would never produce a viable protein out of a random chaotic undirected stochastic chance soup of amino acids!!!!!

(How well did I do the creationist? Do I get 10 points?)

Pretty good, but too many sciency words and not enough flying spittle. I'll give it an 8.

I keep being perplexed. Those who say climate change is false are mostly creationists. How come you think evolution is behind those denialisms? Do you live in a parallel universe?

Heaven forfend, that evolutionists should have to bear the cross for the discredited "science" of Manmade Global Warming. (Nice try, clever switch to "climate change".) If I were truly religious, I would believe that "3 unrelated women in 3 different parts of the country would have similar narratives of Albert Gore raping them", that those must purely be fabrication. And, of course, no charges files, no time in prison "for Nobel Laureates". The better part of valor to not join our multiple prize-winning genius Gore in huckstering Manmade Global Warming.

"I keep being perplexed. Those who say climate change is false are mostly creationists."=====

Exactly, yet you are a "José come lately" to these boards and you may be unfamiliar with some of the stupidity that come from both sides on this. Maybe I'll explain over at your blog.

BTW, I do believe things are environmentally being screwed up and it has a human cause, but then I have none of the Evo-Creo-IDeo lables freely being thrown around here.-----

Negative Entropy:

"How come you think evolution is behind those denialisms?=====

Again you'll have to lok back on some of the posting history here of those who will spew out something stupid if only for the sake of being contrary. Admittedly it won't make sense, but oh well. *wink* -----

Negative Entropy:

"Do you live in a parallel universe?"=====

No I actually live in the real world. But there are clearly people here that have "New Age" leanings and live for definition shell gaming on these boards. Seriously, read some of these kook blogs.

"So, despite the fact that Louis explains evolution via his belief in a omnipotent and omniscient designer, which can supposedly do anything logically possible - like create the entirety of time and space from nothing "=====

Actually there's one problem here. He never did that. Where did you hear or see him reference his god Jesus(or any other diety) ??? The ONLY clue that he hails from the Theistic Evolutionist Kamp comes via the back drop of the Bio-Logos banner hanging in the background as he speaks. Never once did he explain how his god(whoever/whatever it is) used it's guiding intelligence to manipulate the material substrate(which assuming this god already invented) to assemble proteins in such an articulate perfectly sequenced manner for life.

Instead we got the usual canned fable of the organized sequences self-assembling mythology where all the right elements come together into a soup by natural causes(without any interference from intelligence - just physics & chemicals) and defying Crick's & Watson's Central Dogma of the normal real world observed process being informationally driven. What did I miss here ???-----

"Eocene thinks Louis shouldn't think evolution is true because *other people* (atheists) are also think evolution is true and these *other people* supposedly cannot explain evolution without invoking a designer.=====

No he can believe as he wishes, but what I've said all along is that a theistic evolutionist should be detailed and honest in their assessment of the step by step processes that their god(whatever god) used to kick start the evolutionary ball rolling. Unfortunately these cowards(terrified of what atheists and the Secular world will say) never once explain this.

When Cornelius lays out an amazing example of biological complexity in any of these blog subject titles, (admittedly diliberately so) he's illustrating the sophistication and purposed directedness with which these informationally driven nano-molecular machines operate and accomplish what they do in defiance of the undirectedness, unguidance and blind unintelligent chaotic forces which are insisted drive life in the first place. NO ONE has ever given a completely satisfactory answer to these questions of no intelligence allowed and you simply will never be allowed to get away with that.

Unfortunately when we point this out, we get cry babying by self promoting intellectual anonymous Geeks who demonize us by saying we're misrepresenting their religious position. That's "Abiogenesis" they excuse. Evolution is guided and directed and has purpose(other than ideological indoctrination purposes). So sadly we never get a satisfying answer and get labled a heretic for wanting to know the truth without the blind faith requirements.

"Hopefully, your line of logic will make at least some sort of sense."=====

Unfortunately for anyone trying to carry on an intelligent logical conversation with you, we don't have the uncanny ability of a Wiccan or fortune-teller to determine what alter ego multiple personality we are dealing with at any one time or what parallel universe that ego presently resides in at the time of discussion because we can never be certain of what definition shell game of word/terms exist in that said universe. See the dilema ???

Actually there's one problem here. He never did that. Where did you hear or see him reference his god Jesus(or any other diety) ???

The real problem is that you either bought into Cornelius misrepresentation of Louis' video or created one of your own, rather than make an effort to accurately portray Louis' position.

Specifically, Louis was referring to the Irreducible Complexity argument (some things are too complex to have evolved incrementally), not his own views on Evolution and how God was involved.

As such, the absence of his own position isn't a surprise, as you'd like to portray.

However, should you really be interested in Louis' position, there are various videos and blog posts that do elaborate further. To summarize, God supposedly used his omnipotence and omniscience to create a natural process that would eventually result in the biological complexity we observe; just as God supposedly created other natural processes such as time and space out of nothing using his omnipotence and omniscience.

As such, where you and Louis disagree isn't God's ability, but his goals, motives and method of achieving them. In other words, it's all a matter of theology.

Of course, this doesn't bode well for your agenda here, so your best bet was to misrepresent Louis' video as if he had no explanation, despite the fact that his position is reasonably clear by his affliction with the Biologos foundation.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/